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- PDB-1tr4: Solution structure of human oncogenic protein gankyrin -

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Basic information

Entry
Database: PDB / ID: 1tr4
TitleSolution structure of human oncogenic protein gankyrin
Components26S proteasome non-ATPase regulatory subunit 10
KeywordsUNKNOWN FUNCTION / gankyrin / oncoprotein / ankyrin repeats / protein structure
Function / homology
Function and homology information


cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / negative regulation of NF-kappaB transcription factor activity / negative regulation of MAPK cascade / negative regulation of release of cytochrome c from mitochondria / negative regulation of DNA damage response, signal transduction by p53 class mediator ...cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / negative regulation of NF-kappaB transcription factor activity / negative regulation of MAPK cascade / negative regulation of release of cytochrome c from mitochondria / negative regulation of DNA damage response, signal transduction by p53 class mediator / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / cytoskeletal protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / protein localization to plasma membrane / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / positive regulation of cell growth / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / cytoskeleton / Ub-specific processing proteases / neuron projection / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYuan, C. / Li, J. / Mahajan, A. / Poi, M.J. / Byeon, I.J. / Tsai, M.D.
CitationJournal: Biochemistry / Year: 2004
Title: Solution structure of the human oncogenic protein gankyrin containing seven ankyrin repeats and analysis of its structure--function relationship.
Authors: Yuan, C. / Li, J. / Mahajan, A. / Poi, M.J. / Byeon, I.J. / Tsai, M.D.
History
DepositionJun 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 26S proteasome non-ATPase regulatory subunit 10


Theoretical massNumber of molelcules
Total (without water)24,4601
Polymers24,4601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein 26S proteasome non-ATPase regulatory subunit 10 / 26S proteasome regulatory subunit p28 / Gankyrin


Mass: 24459.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD10 / Production host: Escherichia coli (E. coli) / References: UniProt: O75832

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TROSY-type HNCA, HN(CO)CA, HN(CA)CB, CBCA(CO)NH, HNCO
1223D 13C-separated NOESY
1333D 15N-separated NOESY
143residual dipolar coupling
NMR detailsText: Backbone amide residual dipolar coupling experiment was performed in the presence of filamentous Pf1 phage

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Sample preparation

Details
Solution-IDContentsSolvent system
1~0.4 mM gankyrin U-15N,13C,70% 2H5mM HEPES, 1 uM EDTA, 1mM DTT
2~0.4 mM gankyrin U-15N, 13C5mM HEPES, 1 uM EDTA, 1mM DTT
3~0.4 mM gankyrin U-15N5mM HEPES, 1 uM EDTA, 1mM DTT
Sample conditionsIonic strength: < 10 mM salt / pH: 7.4 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
XwinNMR3.1Brukerprocessing
NMRPipe1Delaglioprocessing
NMRView4Johnsondata analysis
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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